I'd encourage you to think more about the "effect" of a port in the actual system, instead of just having the actually values of area into the model. Usually it causes a pressure drop, and you can represent that using an orifice, or flow resistance, or pipe (which has pressure drop model). An area change block may also work, as long as you parametrize it so it provides the right amount of pressure drop for a given flowrate, just like how you would parametrize when using other blocks.
The Doc page for this double-acting actuator shows the diagram under the hood and the isothermal liquid ports are connected to translational mechanical converters. One assumption you see on the Doc page of the converter is that "the flow resistance between the inlet and the interior of the converter is negligible". You can of course add resistance, as you are already trying to do.
